Supporting Information for Proteomics DOI 10.1002/Pmic.200300752

Supporting Information for Proteomics DOI 10.1002/pmic.200300752

Haike Antelmann, Ron Sapolsky, Brian Miller, Eugenio Ferrari, Gopal Chotani, Walter Weyler, Alfred Gaertner and Michael Hecker

Quantitative proteome profiling during the fermentation process of pleiotropic Bacillus subtilis mutants

ª 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.de Fermentation proteome profiling Antelmann et al.

Table I Classification of proteins identified on the cytoplasmic proteome of the B. subtilis parental strain BG2822 grown in 2x SNB medium according to the SubiList code

SubtiLi fun,cat protein st acc. function or homology, EC code, avgX avgY a) b) c) d) e) f) name no. synonym pI Mw 1,1 GcaD BG10113 173,5 173,8 5,65 49290 UDP-N-acetylglucosamine pyrophosphorylase (EC 2.7.7.23) 1,1 GtaB BG10402 UDP-glucose pyrophosphorylase (EC 2.7.7.9.) 338,8 316,3 4,91 32917 1,1 MurA BG11955 UDP-N-acetylglucosamine 1-carboxyvinyl transferase (EC 229,0 209,2 5,45 46537 2.5.1.7) 1,1 MurE BG10223 UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate 184,4 171,7 5,56 54157 ligase (EC 6.3.2.13) 1,1 MurF BG12084 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate- 197,9 185,6 5,33 49557 D-alanyl-D-alanyl ligase (EC 6.3.2.15) 1,2 OppA BG10771 oligopeptide ABC transporter (binding protein) 264,1 165,7 5,72 61318 1,2 OppD BG10774 oligopeptide ABC transporter (ATP-binding protein) 124,6 223,3 6,02 39606 1,2 RbsB BG10881 ribose ABC transporter (ribose-binding protein) 6.14 32073 1,2 YciC BG12021 probably part of a low-affinity pathway of zinc transport 4,40 45145 1,2 YqiX BG11727 similar to amino acid ABC transporter (binding protein) 373,0 359,3 5,09 28162 1,2 YurY BG14011 similar to ABC transporter (ATP-binding protein) 402,5 344,7 4,62 28879 1,2 YvdG BG12416 similar to maltose/maltodextrin-binding protein 387,0 212,1 4,91 45437, 1,4 AtpA BG10819 ATP synthase alpha chain (EC 3.6.1.34) 318,3 182,7 5,04 54432 1,4 AtpD BG10821 ATP synthase beta chain (EC 3.6.1.34) 423,1 191,0 4,61 51255 1,4 AtpF BG10817

ATP synthase (subunit b) (EC 3.6.1.34) 4,92 19064 1,4 YjlD BG13203 similar to NADH dehydrogenase 63,5 247,9 6,29 41794 1,5 Hag BG10655 flagellin 376,0 263,3 4,78 32472 1,6 FtsY BG11539 signal recognition particle (docking protein) 288,9 253,0 5,08 36187 1,6 SecA BG10741 preprotein translocase subunit (ATPase) 233,8 88,8 5,34 95334 1,7 DivIVa BG11835 cell-division initiation protein (septum placement) 4,85 19196 1,7 Gid BG11008 glucose- inhibited division protein 140,4 188,3 5,76 47899 1,8 Spo0M BG12229 disruption or overproduction has negative effects on 477,0 298,6 4,28 29557 sporulation; syn YgaI 1,8 SpoIVA BG10275 required for proper spore cortex formation and coat assembly; 414,7 161,4 4,55 55007 syn SpoVP 1,8 SpoVG BG10112 required for spore cortex synthesis 274,7 583,5 5,11 10755 2,1,1 AckA BG10813 acetate kinase (EC 2.7.2.1) 282,8 224,2 5,19 42976 2,1,1 AcoA BG12558 acetoin dehydrogenase E1 component (TPP-dependent alpha 338,8 249,0 4,91 35912 subunit); syn YfjK 2,1,1 AcoB BG12559 acetoin dehydrogenase E1 component (TPP-dependent beta 456,8 253,3 4,4 36689 subunit); syn YfjJ 2,1,1 AcsA-C1 BG10370 acetyl CoA synthetase (EC 6.2.1.1) 5,55 64717 2,1,1 AcsA-C2 BG10370 acetyl CoA synthetase (EC 6.2.1.1) 5,55 64717 2,1,1 GlpK BG10187 glycerol kinase (EC 2.7.1.30) 346,3 180,8 4,98 54910 2,1,1 IolC BG11119 similar to fructokinases, 2-keto-3-deoxygluconate kinases and 365,1 213,4 4,78 35476 ribokinases of bacteria 2,1,1 IolD BG11120 myo-inositol catabolism 285,2 112,3 5,01 63960 2,1,1 IolH BG11123 myoinositol catabolism 328,3 309,6 4,99 33370 2,1,1 IolI BG11124 similar to glyoxylate-induced protein of H. influenzae 410,3 332,6 4,66 31503 2,1,1 IolS BG11363 similar to auxin-induced protein of common tobacco, similar to 235,8 268,4 5,38 35014 oxidoreductases; syn YxbF 2,1,1 MalA BG11839 6-phospho alpha glucosidase (EC 3.2.1.122), syn GlvA 4,74 50384

30 Fermentation proteome profiling Antelmann et al.

2,1,1 MalL BG12421 oligo-1,4-1,6-alpha-glucosidase (sucrase-maltase-isomaltase) 338,7 149,2 4,98 65906 2,1,1 Pta BG10634 phosphate acetyltransferase (EC 2.3.1.8.) 415,7 283,7 4,65 34636 2,1,1 PtsH BG10200 phosphocarrier protein of phosphotransferase system 377,6 573,1 4,58 9051 2,1,1 RbsK BG10877 ribokinase (EC 2.7.1.15) 407,2 245,0 4,61 30986 2,1,1 YdjL BG12803 similar to L-iditol 2-dehydrogenase 358,9 213,5 4,8 37186 2,1,1 YhfE BG13051 similar to glucanase 131,6 213,2 5,88 38579 2,1,1 YjdE BG13177 similar to mannose-6-phosphate isomerase 260,0 236,9 5,27 35848 2,1,1 YqiQ BG11720 unknown; similar to phosphoenolpyruvate mutase 5.279 32942 2,1,1 YsdC BG12317 similar to endo-1,4-beta-glucanase 202,4 233,8 5,55 39059 2,1,1 YtoP BG13898 similar to endo-1,4-beta-glucanase 173,2 260,4 5,65 39079 2,1,1 YvcT BG12409 similar to glycerate dehydrogenase 306,8 291,3 5,09 36463 2,1,2 Eno BG10899 enolase (EC 4.2.1.11) 436,6 210,2 4,49 46418 2,1,2 FbaA BG10412 fructose-1,6-bisphosphate aldolase (EC 4.1.2.13) 306,0 300,0 5,03 30248 2,1,2 GapA BG10827 glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) 298,9 236,6 5,03 35676 2,1,2 GapB BG12592 glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) 14,6 248,8 6,45 37320 2,1,2 PckA BG11841 phosphoenolpyruvate carboxykinase (EC 4.1.1.49) 295,1 155,5 5,11 58128 2,1,2 PdhA BG10207 pyruvate dehydrogenase (E1 alpha subunit) (EC 1.2.4.1) 114,6 241,0 5,84 41390 2,1,2 PdhB BG10208 pyruvate dehydrogenase (E1 beta subunit) (EC 1.2.4.1) 432,2 265,6 4,55 35320 2,1,2 PdhC BG10209 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase 357,9 151,6 4,86 47376 E2 subunit) (EC 2.3.1.12) 2,1,2 PdhD BG10210 dihydrolipoamide dehydrogenase E3 subunit of both pyruvate 373,8 157,4 4,76 49567 dehydrogenase and 2-oxoglutarate dehydrogenase complexes (EC 1.8.1.4) 2,1,2 Pfk BG12644 6-phosphofructokinase (EC 2.7.1.11) 62,5 280,4 6,14 34100 2,1,2 Pgi BG11720 glucose-6-phosphate isomerase 5.28 32942 2,1,2 Pgk BG11062 phosphoglycerate kinase (EC 2.7.2.3) 379,4 214,2 4,77 42030 2,1,2 Pgm BG10898 phosphoglycerate mutase (EC 5.4.2.1) 278,0 137,6 5,21 56140 2,1,2 PycA BG12660 pyruvate carboxylase (EC 6.4.1.1) 237,5 63,7 5,41 127721 2,1,2 Tkt BG11247 transketolase (EC 2.2.1.1) 361,7 108,6 4,8 72163 2,1,2 Tpi BG10897 triose phosphate isomerase (EC 5.3.1.1) 367,1 323,2 4,79 26880 2,1,2 YwjH BG10413 similar to transaldolase 180,8 407,4 5,61 19830 2,1,2 Zwf BG11739 unknown; similar to glucose-6-phosphate 1-dehydrogenase 5,28 55492 (pentose phosphate) 2,1,3 CitB BG10478 aconitate hydratase (EC 4.2.1.3) 333,1 69,5 4,9 99136 2,1,3 CitC BG10856 isocitrate dehydrogenase (EC 1.1.1.42) 373,0 221,9 4,83 46255 2,1,3 CitG BG10384 fumarate hydratase (EC 4.2.1.2) 209,9 199,1 5,47 50365 2,1,3 CitH BG11386 malate dehydrogenase (EC 1.1.1.37) 388,1 283,6 4,73 33490 2,1,3 CitZ BG10855 citrate synthase II (EC 4.1.3.7) 221,2 240,2 5,45 41569 2,1,3 OdhA BG10272 2-oxoglutarate dehydrogenase (E1 subunit) (EC 1.2.4.2) 205,2 73,8 5,84 105093 2,1,3 SdhA BG10352 succinate dehydrogenase (flavoprotein subunit) (EC 1.3.99.1) 204,3 134,9 5,71 65174 2,1,3 SucC BG12680 succinyl-CoA synthetase (beta subunit) ( EC 6.2.1.5) 357,8 237,7 4,85 41212 2,1,3 SucD BG12681 succinyl-CoA synthetase (alpha subunit) (EC 6.2.1.5) 181,0 304,8 5,59 31229 2,2 Ald BG10468 L-alanine dehydrogenase (EC 1.4.1.1) 281,2 212,6 5,12 39525 2,2 AnsB BG10301 L-aspartase (EC 4.3.1.1) 196,8 173,4 5,69 52386 2,2 ArgC BG10191 N-acetylglutamate gamma semialdehyde dehydrogenase (EC 295,1 248,9 5,17 37917 1.2.1.38) 2,2 ArgD BG10194 N-acetylornithine aminotransferase (EC 2.6.1.11) 87,2 246,8 5,93 40735 2,2 ArgF BG10197 ornithine carbamoyltransferase (EC 2.1.3.3) 320,6 224,0 4,96 34509 2,2 ArgG BG12570 argininosuccinate synthase (EC 6.3.4.5) 315,3 197,5 5,03 44657 2,2 AroA BG10375 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (EC 234,6 241,3 5,34 39382 4.1.2.15) and chorismate mutase (EC 5.4.99.5) 2,2 AroF BG10284 5-enolpyruvoylshikimate-3-phosphate phospholyase, 100,0 216,5 6,58 39812 chorismate synthase (EC 4.6.1.4) 2,2 Asd BG10783 aspartate semialdehyde dehydrogenase (EC 1.2.1.11) 320,3 216,2 4,97 37690

31 Fermentation proteome profiling Antelmann et al.

2,2 AspB BG11513 aspartate aminotransferase (EC 2.6.1.1) 230,5 216,4 5,3 42928 2,2 CarB BG10196

carbamoyl-phosphate transferase-arginine (subunit B) 4,71 112746 2,2 CysK BG10136 cysteine synthetase A (EC 4.2.99.8) 189,9 319,6 5,49 32666 2,2 DapB BG11207 dihydrodipicolinate reductase (EC 1.3.1.26) 5.06 29336

2,2 GlnA BG10425 glutamine synthetase (EC 6.3.1.2) 350,3 189,2 4,87 50113 2,2 GlyA BG10944 serine hydroxymethyl transferase (EC 2.1.2.1) 216,5 206,7 5,48 45328

2,2 GudB BG11435 glutamate dehydrogenase (inactive) 5.58 47048 2,2 Hom BG10460 homoserine dehydrogenase (EC 1.1.1.3) 341,5 160,6 4,9 47331 2,2 HutI BG11100 imidazolone-5-propionate hydrolase (EC 3.5.2.7) 273,7 218,4 5,21 45402 2,2 HutU BG10668 urocanase (EC 4.2.1.49) 176,1 146,7 5,66 60428 2,2 IlvA BG10673 threonine dehydratase (EC 4.2.1.16) 207,1 194,5 5,54 46490 2,2 IlvC BG10672 ketol-acid reductoisomerase (EC 1.1.1.86) 226,8 259,3 5,37 37302 2,2 Kbl BG12610 2-amino-3-ketobutyrate CoA ligase (glycine acetyl transferase) 33,4 224,5 6,25 43124 (EC 2.3.1.29) 2,2 LeuC BG11949 3-isopropylmalate dehydratase (large subunit) (EC 4.2.1.33) 64,3 190,9 6,13 52225

2,2 LeuD BG11950 3-isopropylmalate dehydratase (small subunit) 4,58 22875 2,2 MetK BG11840 S-adenosylmethionine synthetase (EC 2.5.1.6) 310,4 182,7 5,03 43882 2,2 MmsA BG11117 methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27), 5,14 53285 syn IolA 2,2 RocA BG10622 pyrroline-5 carboxylate dehydrogenase (EC 1.5.1.12) 187,6 163,1 5,58 56151 2,2 RocD BG10722 ornithine aminotransferase (EC 2.6.1.13) 341,3 221,2 4,89 43601 2,2 RocF BG10932 arginase (EC 3.5.3.1) 346,1 311,6 4,93 32001 2,2 RocG BG10621 glutamate dehydrogenase 91,5 220,7 6,28 46475 2,2 SerA BG10509 phosphoglycerate dehydrogenase (EC 1.1.1.95) 173,6 153,8 5,62 56946 2,2 SpeB BG12461 agmatinase 4.77 32264 2,2 ThrC BG10461 threonine synthase (EC 4.2.99.2) 270,8 255,9 5,19 37307 2,2 YcgN BG12012 similar to 1-pyrroline-5-carboxylate dehydrogenase 240,1 165,2 5,37 56320 2,2 YheM BG13045 similar to D-alanine aminotransferase 345,8 277,0 4,87 31030 2,2 YwaA BG10546 similar to branched-chain amino acid aminotransferase 330,9 249,0 4,95 40164 2,3 Cmk BG11004 cytidylate kinase (EC 2.7.4.14) 327,1 356,6 4,99 24948 2,3 DeoD BG12581 purine nucleoside phosphorylase (EC 2.4.2.1) 334,3 377,3 4,97 25229 2,3 Dra BG10983 deoxyribose-phosphate aldolase (EC 4.1.2.4 360,9 368,9 4,92 22064 2,3 GuaA BG10647 GMP synthetase (EC 6.3.5.2) 387,3 154,5 4,75 57782 2,3 GuaB BG10073 inosine-5'-monophosphate dehydrogenase (EC 1.1.1.205) 63,3 179,5 6,17 52824 2,3 Ndk BG10282 nucleoside diphosphate kinase (EC 2.7.4.6) 179,4 558,4 5,57 16816 2,3 Pnp BG11330 purine nucleoside phosphorylase (EC 2.4.2.1) 359,4 350,4 4,86 28976 2,3 PnpA BG11491 polynucleotide phosphorylase (PNPase) (EC 2.7.7.8) 344,8 104,8 4,89 77280 2,3 Prs BG10114 phosphoribosyl pyrophosphate synthetase (EC 2.7.6.1); syn 108,5 302,1 5,9 34714 KprS 2,3 PurA BG10002 adenylosuccinate synthetase (EC 6.3.4.4) 216,7 188,7 5,46 47509 2,3 PurB BG10702 adenylosuccinate lyase (EC 4.3.2.2) 142,7 216,5 5,82 49320 2,3 PyrAB BG10716 carbamoyl-phosphate synthetase (catalytic subunit) (EC 367,2 61,1 4,78 117440 6.3.5.5) 2,3 SmbA BG12675 uridylate kinase (EC 2.7.4.-) 300,8 356,5 4,87 25841 2,3 YpfD BG11005 similar to ribosomal protein S1 homolog 429,6 197,0 4,57 42244 2,4 Bcd BG11723 leucine dehydrogenase in branched-chain fatty acid 333,2 221,0 4,94 39833 biosynthesis, NADH-dependent decarboxylase inhibitor; syn Bkd 2,4 PlsX BG11843 involved in fatty acid/phospholipid synthesis; syn YlpD 190,5 239,0 5,49 35607 2,4 YjbW BG13152 similar to enoyl-acyl-carrier protein reductase 175,7 337,9 5,72 28905 2,4 YoxD BG11048 similar to 3-oxoacyl- acyl-carrier protein reductase 241,3 383,5 5,33 25150

32 Fermentation proteome profiling Antelmann et al.

2,4 YqiV BG11725 probable branched-chain alpha-keto acid dehydrogenase E3 329,6 175,0 4,89 48510 subunit (dihydrolipoamide dehydrogenase); syn Bkd 2,4 YvrD BG14144 similar to ketoacyl-carrier protein reductase 393,2 353,2 4,68 28070 2,5 DhaS BG12582 aldehyde dehydrogenase 301,7 159,5 5,02 53713 2,5 DhbE BG11711 2,3-dihydroxybenzoate-AMP ligase (enterobactin synthetase component E) 5,68 59758 2,5 FolD BG11943 methylenetetrahydrofolate dehydrogenase (EC 1.5.1.5) and 169,0 331,8 5,6 30534 methenyltetrahydrofolate cyclohydrolase (EC 3.5.4.9) + 2,5 NadE BG10184 NH3 dependent NAD synthetase (EC 6.3.5.1) 330,5 274,9 4,89 30244 2,5 YhxA BG13271 similar to adenosylmethionine-8-amino-7-oxononanoate 178,6 214,0 5,64 49707 aminotransferase 2,5 YjbT BG13149 unknown; similar to thiamin biosynthesis. hydroxyethylthiazole 4,72 26872 phosphate biosynthesis 2,5 YodC BG11337 similar to nitroreductase 250,8 396,4 5,27 22194 2,6 YybQ BG13378 putative exopolyphosphatase 440,1 284,2 4,51 33834 2,7 YlnB BG14099 probably part of the S box regulon, similar to sulfate 218,1 212,5 5,65 42725 adenylyltransferase

3,1 Ssb BG10048 single-strand DNA-binding protein 4.822 18598 3,4 GyrB BG10070 DNA gyrase (subunit B) 5,38 71324 3,5,1 YvyD BG10376 similar to σ 54 modulation factors 278,1 383,9 5,18 21834 3,5,2 CcpA BG10968 transcriptional regulator of carbon catabolite repression 286,8 269,2 5,06 36784 3,5,2 CodY BG10393 pleiotropic transcriptional repressor 352,4 334,5 4,75 28862 3,5,2 DegU BG10393 two-component response regulator 181,2 345,6 5,6 25718 3,5,2 DegU-P BG10110 two-component response regulator 181,2 345,6 5,6 25718 3,5,2 ResD two-component response regulator involved in aerobic and BG10534 anaerobic respiration 5.63 27336 3,5,2 YugG BG12361 unknown; similar to transcriptional regulator (Lrp/AsnC family). 4,89 18616 transcriptional regulator of the alaRT operon 3,5,3 GreA BG10732 transcription elongation factor 426,5 430,1 4,48 17129 3,5,3 RpoA BG10728 RNA polymerase (alpha subunit) (EC 2.7.7.6) 418,0 218,0 4,59 34644 3,5,3 RpoB BG12363 RNA polymerase (beta subunit) (EC 2.7.7.6) 373,5 49,8 4,73 133376 3,6 YugI BG11220 similar to RNA-binding motif of S1 and PnpA; syn Gsp13 5,92 14143 3,7,1 RplJ BG10726 ribosomal protein L10 (BL5) 277,2 503,1 5,49 17885 3,7,1 RplL BG19004 ribosomal protein L7/L12 (BL9) 468,5 580,3 4,36 12611 3,7,1 RpsF BG10958 ribosomal protein S6 (BS9) 322,3 621,5 4,99 10986 3,7,2 AsnS BG12572 asparaginyl-tRNA synthetase (EC 6.1.1.22) 281,2 162,6 5,12 48920 3,7,2 AspS BG12839 aspartyl-tRNA synthetase (EC 6.1.1.12) 396,3 139,8 4,65 65799 3,7,2 GatA BG12840 glutamyl-tRNA(Gln) amidotransferase (subunit A) 277,8 177,5 5,24 52497 3,7,2 GatB BG10154 glutamyl-tRNA(Gln) amidotransferase (subunit B) 351,9 176,6 4,94 46909 3,7,2 GltX BG11658 glutamyl-tRNA synthetase (EC 6.1.1.17) 299,9 154,8 5,02 55555 3,7,2 GlyS BG12605 glycyl-tRNA-synthetase beta chain (EC 6.1.1.14) 306,9 108,0 4,97 76051 3,7,2 HisS BG11792 histidyl-tRNA synthetase (EC 6.1.1.21) 272,9 212,0 5,22 47968 3,7,2 IleS BG10676 isoleucyl-tRNA synthetase 270,1 67,9 5,19 104584 3,7,2 LeuS BG10144 leucyl-tRNA synthetase 357,1 83,7 4,86 91350 3,7,2 MetS BG10875 methionyl-tRNA synthetase 319,2 100,6 4,96 76007 3,7,2 PheT BG12659 phenylalanyl-tRNA-synthetase beta chain (EC 6.1.1.20) 354,4 79,5 4,86 87756 3,7,2 ProS BG10077 prolyl-tRNA synthetase 320,8 123,0 5,01 63131 3,7,2 SerS BG10362 seryl-tRNA synthetase (EC 6.1.1.11) 266,1 175,3 5,19 48678 3,7,2 ThrS BG11937 threonyl-tRNA synthetase (EC 6.1.1.3) 260,4 111,2 5,21 73335 3,7,2 ThrZ BG10421 threonyl-tRNA synthetase (minor) 5.753 73195 3,7,3 Fmt BG11939 methionyl-tRNA formyltransferase (EC 2.1.2.9) 157,9 269,7 5,61 34480 3,7,4 EF-G BG19025 elongation factor of translation 4,62 76360 3,7,4 EF-Ts BG11056 elongation factor of translation 324,1 299,1 4,98 32200 3,7,4 EF-Tu BG10441 elongation factor of translation 381,3 196,7 4,72 43432 3,7,4 YlaG BG12587 similar to GTP binding elongation factor (translation) 312,0 99,7 4,97 68212

33 Fermentation proteome profiling Antelmann et al.

3,7,5 Frr BG11789 ribosome recycling factor 242,6 402,2 5,33 20621

3,8 AmhX BG10512 amidohydrolase 6,12 42370 3,8 PpiB BG11708 peptidyl-prolyl isomerase (EC 5.2.1.8) 224,0 539,6 5,47 15115 3,8 PrkA BG10804 serine protein kinase 5,46 72706 3,9 DnaK BG10423 chaperone 423,6 119,8 4,57 65826 3,9 GroEL BG10148 chaperone 428,8 143,5 4,53 57252 3,9 GroES BG10422 class I heat-shock protein (chaperonin) 4.6 10037 3,9 Tig BG10664 trigger factor (prolyl isomerase) 496,7 155,8 4,22 47324 4,1 ClpC BG12578 ATPase subunit of Clp protease; syn MecB 148,8 102,8 5,75 89927 4,1 ClpP BG10967 proteolytic subunit of Clp protease (EC 3.4.21.92) 314,5 400,8 5,01 21536

4,1 CspD BG10115 cold-shock protein 4.31 7173 4,1 GrpE BG10826 chaperone 487,5 336,1 4,26 21537 4,1 HtpG BG10338 class IV heat-shock protein; syn YxbB 399,5 114,8 4,67 72078 4,2 AhpC BG11204 alkyl hydroperoxide reductase (small subunit) (EC 1.6.4.-) 497,7 426,6 4,28 20482 4,2 AhpF BG10849 alkyl hydroperoxide reductase (large subunit) (EC 1.6.99.3) 400,6 175,1 4,71 54705 4,2 KatA BG11102 catalase 1 (EC 1.11.1.6) 97,1 156,7 6,15 54567 4,2 SodA BG12767 superoxide dismutase (EC 1.15.1.1) 337,6 401,6 4,96 25143 4,2 YceC BG12768 similar to tellurium resistance protein 234,8 372,7 5,31 21678 4,2 YceD BG12772 similar to tellurium resistance protein; syn TerD 488,1 390,0 4,29 20549 4,2 YceH BG12071 similar to toxic anion resistance protein 155,3 240,7 5,74 41512 4,2 YqfP BG13855 similar to penicillin tolerance 135,8 273,8 5,61 34770 4,2 YtgI BG10171 similar to thiol peroxidase 433,1 463,8 4,7 18072 4,3 SrfAD BG11494 surfactin synthetase ; syn ComL 249,8 321,0 5,22 27472 4,6 YbaL BG10951 similar to ATP-binding Mrp-like protein; methyl 258,5 225,3 5,23 38481 methanesulfonate-sensitive phenotype 5,1 YoxA BG11701 similar to unknown proteins from B. subtilis 197,4 266,7 5,6 37073 5,1 YqjL BG11741 unknown; similar to unknown proteins from B. subtilis 6.56 28021 5,2 YkqC BG11814 similar to unknown proteins 122,3 152,7 5,9 61344 5,2 YqkF BG12310 similar to unknown proteins 295,0 296,4 5,13 34563

5,2 YugU BG12373 unknown; similar to unknown proteins 6.59 16166 5,2 YurU BG14010 similar to unknown proteins 324,8 151,6 4,95 52561 5,2 YurX BG14057 similar to unknown proteins 333,5 156,7 4,95 48130 5,2 YvbY BG12448 similar to proteins of unknown function 274,1 352,7 5,16 26128 5,2 YvfW BG12053 similar to unknown proteins 124,7 170,0 5,84 53306 6 YjcG BG12337 unknown 165,5 435,2 5,57 19518 6 YxbC BG11353 unknown 411,5 233,9 4,58 37302 a) All 211 cytoplasmic proteins labeled in Fig.2a were identified in the cytoplasmic proteome of B. subtilis wild type BG2822 grown in 2x SNB medium at the transition phase (t2, Fig.1). These proteins were classified according to the SubtiList functional catogories (http://genolist.pasteur.fr/SubtiList/). In three cases there are different names of genes and their corresponding products (tufA and EF- Tu, fus and EF-G, tsf and EF-Ts). b) Specific protein names, accession numbers as well as the theoretical isoelectric points (e) and molecular weight (f) were also derived according to the SubtiList database. c) AvgX indicates the average X- coordinates calculated from 12 different 2D gels which corresponds to the practical isoelectric point. d) AvgY indicates the average Y- coordinates calculated from 12 different 2D gels which corresponds to the practical molecular weight. Note, that all proteins that have no X,Y, coordinates were failed to be detected by the spot detection algorythm of the Decodon Delta 2D software.

34